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FROM ubuntu:20.04
LABEL base_image="ubuntu:20.04"
LABEL version="2.0"
LABEL maintainer="Kevin Nathanael Ramanto"
LABEL maintainer.email="[email protected]"
ENV TZ=Asia/Singapore
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
&& echo $TZ > /etc/timezone
RUN export DEBIAN_FRONTEND=noninteractive \
&& apt-get update -y \
&& apt-get -y --no-install-recommends install git python-is-python3 python3-pip \
&& apt-get autoclean -y \
&& apt-get install -y apt-utils unzip wget build-essential zlib1g-dev libbz2-dev liblzma-dev libmath-libm-perl libpthread-stubs0-dev curl python3-pycurl git git-lfs gawk libncurses-dev libboost-all-dev libgtest-dev cmake libssl-dev libcurl3-dev\
&& pip install pandas numpy scipy argparse matplotlib
RUN wget --max-redirect=1 https://github.com/samtools/bcftools/releases/download/1.15.1/bcftools-1.15.1.tar.bz2 \
&& tar -xf bcftools-1.15.1.tar.bz2 \
&& mkdir bcftools \
&& cd bcftools-1.15.1 \
&& ./configure --prefix=/bcftools \
&& make \
&& make install \
&& cd ../ \
&& rm bcftools-1.15.1.tar.bz2 \
&& apt-get install -y tabix
RUN mkdir GLIMPSE \
&& cd GLIMPSE \
&& wget --max-redirect=1 https://github.com/odelaneau/GLIMPSE/releases/download/v2.0.0/GLIMPSE2_phase_static \
&& wget --max-redirect=1 https://github.com/odelaneau/GLIMPSE/releases/download/v2.0.0/GLIMPSE2_ligate_static \
&& wget --max-redirect=1 https://github.com/odelaneau/GLIMPSE/releases/download/v2.0.0/GLIMPSE2_split_reference_static \
&& wget --max-redirect=1 https://github.com/odelaneau/GLIMPSE/releases/download/v2.0.0/GLIMPSE2_chunk_static \
&& mv GLIMPSE2_phase_static GLIMPSE2_phase \
&& mv GLIMPSE2_ligate_static GLIMPSE2_ligate \
&& mv GLIMPSE2_split_reference_static GLIMPSE2_split_reference \
&& mv GLIMPSE2_chunk_static GLIMPSE2_chunk \
&& chmod +x GLIMPSE2_phase \
&& chmod +x GLIMPSE2_ligate \
&& chmod +x GLIMPSE2_split_reference \
&& chmod +x GLIMPSE2_chunk \
&& cd ../
RUN mkdir wrapper
COPY ./GLIMPSE_phase.py /wrapper
RUN pip install awscli
ENV PATH="$PATH:/bcftools/bin"
ENV PATH="$PATH:/GLIMPSE/"
WORKDIR /data